PDBsum entry: 3fpd

Transferase

PDB id: 3fpd

Contents

Protein chains

261 a.a. *

Ligands

SAH ×2

Q4A ×2

Metals

_ZN ×8

Waters ×119

* Residue conservation analysis

PDB id:

3fpd

Name:

Transferase

Title:

G9a-like protein lysine methyltransferase inhibition by bix- 01294

Structure:

Histone-lysine n-methyltransferase, h3 lysine-9 specific 5. Chain: a, b. Fragment: unp residues 975-1235, set domain. Synonym: histone h3-k9 methyltransferase 5, h3-k9-hmtase 5, euchromatic histone-lysine n-methyltransferase 1, eu- hmtase1, g9a-like protein 1, glp1, lysine n- methyltransferase 1d. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ehmt1, euhmtase1, kiaa1876, kmt1d. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.40Å R-factor: 0.221 R-free: 0.262

Authors:

Y.Chang,X.Zhang,J.R.Horton,X.Cheng

Key ref:

Y.Chang et al. (2009). Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294. Nat Struct Biol, 16, 312-317. PubMed id: 19219047 DOI: 10.1038/nsmb.1560

Date:

05-Jan-09 Release date: 17-Feb-09

Protein chains

Q9H9B1  (EHMT1_HUMAN) -  Histone-lysine N-methyltransferase EHMT1

Seq: 1298 a.a.

Struc: 261 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.43 - Histone-lysine N-methyltransferase.
• Reaction: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N₆-methyl-L-lysine-[histone]

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine (Bound ligand (Het Group name = SAH) corresponds exactly) + N(6)-methyl-L-lysine-[histone]

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (1 term)
• Biological process: chromatin modification (1 term)
• Biochemical function: zinc ion binding (2 terms)

Added reference

DOI no: 10.1038/nsmb.1560

Nat Struct Biol 16:312-317 (2009)

PubMed id: 19219047

Structural basis for G9a-like protein lysine methyltransferase inhibition by BIX-01294.

Y.Chang, X.Zhang, J.R.Horton, A.K.Upadhyay, A.Spannhoff, J.Liu, J.P.Snyder, M.T.Bedford, X.Cheng.

ABSTRACT

Histone lysine methylation is an important epigenetic mark that regulates gene expression and chromatin organization. G9a and G9a-like protein (GLP) are euchromatin-associated methyltransferases that repress transcription by methylating histone H3 Lys9. BIX-01294 was originally identified as a G9a inhibitor during a chemical library screen of small molecules and has previously been used in the generation of induced pluripotent stem cells. Here we present the crystal structure of the catalytic SET domain of GLP in complex with BIX-01294 and S-adenosyl-L-homocysteine. The inhibitor is bound in the substrate peptide groove at the location where the histone H3 residues N-terminal to the target lysine lie in the previously solved structure of the complex with histone peptide. The inhibitor resembles the bound conformation of histone H3 Lys4 to Arg8, and is positioned in place by residues specific for G9a and GLP through specific interactions.

Selected figure(s)

Figure 1.
(a) Progression of methylation as a function of reaction time. The arrows point to the conditions used for subsequent inhibition studies. (b) The inhibition on G9a and GLP by various concentrations of BIX-01294. (c) Variation in the relative abundance of each peptide species (me0, me1 and me2) as a function of BIX-01294 concentration. (d) Ras-mediated epigenetic silencing of Fas is derepressed with both BIX-01294 (BIX) and 5-aza treatments. (e) Methylation of DNMT1 by G9a and GLP and inhibition by BIX-01294; the autoradiography image and relative activity by TCA counts. Error bars in b, c and e indicate s.d. for two duplicated measurements.

Figure 2.
(a) Structure of the GLP SET domain. (b) AdoHcy and BIX-01294 bind in two distinctive pockets. (c,d) BIX-01294 binds in the substrate peptide binding groove (c), which is occupied by H3K4–H3R8 (d; PDB 2RFI^12). (e) Superimposition of H3 peptide (yellow) and BIX-01294. (f) Water molecules (small red spheres) occupy the target lysine binding channel.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 312-317) copyright 2009.

Figures were selected by the author.

Author's comment

In panel Figure 1e, the concentration of inhibitor is in uM (micro M).